Metabolomics is a powerful tool for the study of biological systems. Besides analytical techniques, cell harvest and extraction are critical steps, especially when studying encapsulated streptococci. We have compared four different harvesting techniques for biomass from liquid culture of the hyaluronic acid (HA)-producing bacterium Streptococcus zooepidemicus. The best method for cell separation was quick (2 min) centrifugation, which allowed efficient medium removal and enabled quantification of the broadest range of sugar metabolites. Unlike observations for other microbes, changes in metabolite pools due to a delay of extraction by the centrifugation were not observed, so metabolite levels accurately reflected the metabolome at the point of cell harvest. A hypothesis is that the capsule itself isolates the cells from the surroundings and still supports it with nutrients during the harvest. Quantification of sugar phosphates and nucleotide sugars was performed using high-performance anion exchange chromatography combined with pulsed amperometric detection, achieving limits of quantification of 2.5 pmol for sugar phosphates and 5 pmol on column for nucleotide sugars. Intracellular pool sizes for intermediates of the HA pathway under production conditions ranged from 0.2 to 0.5 micromol/g cell dry weight.